Cheating and cycling have a long history together. Maurice Garin, the winner of the first Tour de France, in 1903, was disqualified the following year after he was caught taking the train. In the early days, cyclists were essentially lab rats: They raced on caffeine, cocaine, strychnine, amphetamines, nitroglycerine, ether, even brandy. In 2004, one French rider admitted to rubbing salt on his testicles until they bled so he’d be allowed to use cortisone.

In August 2010, a grand jury convened in Los Angeles to decide whether to indict Armstrong on federal charges. The investigation was led by an FDA agent named Jeff Novitzky, most famous for investigating Barry Bonds, Roger Clemens, and the sprinter Marion Jones. The biggest issue was whether Armstrong had used a drug called erythropoietin, or EPO, an artificial hormone that boosts the production of red blood cells, which deliver oxygen to the muscles. He’d been given EPO as part of his cancer treatment in 1996. But if he were found to have taken EPO later on, when he was racing again – and, crucially, to have lied about it while accepting sponsorship money from the U.S. Postal Service, a federal agency – he could be brought up on charges of conspiracy and fraud.

Armstrong had been under investigation before. After a French TV crew filmed two men from his team dumping bags of medical waste on a roadside, French authorities launched a two-year doping inquiry, which was closed due to a lack of evidence. But this latest inquiry was based on more than trash. Novitzky reportedly contacted several of Armstrong’s teammates, including Floyd Landis, Tyler Hamilton, and George Hincapie, whom Armstrong once described as, "like a brother to me." The most damning charges came from Landis and Hamilton, who appeared on Nightline and 60 Minutes, respectively, to accuse Armstrong of doping. Armstrong vehemently denied it, pointing out that both were admitted cheaters and liars. Still, their accusations had the advantage of specificity. It was like something out of a spy novel: midnight deliveries of mysterious white bags; secret cellphones; code words. They painted a picture of a drug ring, with Armstrong as its kingpin.

Armstrong has always prized loyalty, and this represented a serious crack in his wall of cycling omerta. He and Hamilton were never especially close, but for a while, Landis was Armstrong’s protégé. I ask him if he felt betrayed. "I’m not even going to comment on those guys, because it opens me up to civil cases and stuff," he says. "But I wasn’t surprised. The truth is, one of the riders" – he means Landis – "was making threats for years. After a while, I was like, ‘You know what? Go ahead – do it or don’t. Leave me alone.’ "

In public, Armstrong struck a defiant tone. He lawyered up, hiring Mark Fabiani, who defended Goldman Sachs during its SEC fraud case and the Clintons during Whitewater. Armstrong repeated his standard lines: He was the most tested athlete in history, he’d never had a positive test. Sometimes he needled the Feds back: When Novitzky flew to Interpol’s headquarters in Lyons to meet with European police officials, Armstrong posted a taunt on Twitter: "Hey, Jeff: Como estan los hoteles de quatro estrellas y el classe de business in el aeroplano? Que mas necesitan?" (Translation: "Hey, Jeff: How are the four-star hotels and business-class flights? What more do you need?")

But today, with the benefit of hindsight, Armstrong admits he was scared. "I compare most things to cancer," he says. "When you’re first diagnosed, you don’t know what you’re up against. You start to learn more, and you get a sense of where you are. But this was completely different. You have no idea who your foe is. You have no way to measure where you are in the fight. You’re just lost."

For Anna, not knowing was the hardest part: "I was like, ‘OK, tell us what’s going to happen. Do you want to go to court? Do you want to take away Tour titles?’ You never knew when it was going to end," she says. "We were like, ‘Are we going to live with this situation for six months? Two years? Ten years?’ "

Most of what Armstrong knew he had learned from the press, where the case was, as he puts it, "being leaked to the media like a screen door." Sometimes he’d open his New York Times to see an article on the top of the front page, where, he says, "the real stories are – the economy, the election, Syria. Those are the days you’re like, ‘Dude, what the fuck is going on?’ "

In July, his legal team filed a motion to protest the leaks, claiming that even if Armstrong was never charged, the leaks "guarantee that [his] reputation will have been permanently damaged."

"I’m sure it has been," Armstrong says. "But I’m OK with that. We all want to be loved, we all want to be respected, we all want to be thought of as fair and ethical and admirable men. But very few people are unimpeachable. I’ve resigned myself to the fact that there are always going to be questions."

In the end, he says the investigation was "the most frustrating and confusing thing I’ve ever been through. I was miserable. If people think I was an asshole before. . . ." He sighs. "There were days where you just damn near crack – personally and privately." He says he didn’t see a therapist, "although it crossed my mind." "I wish he would have," Korioth says. "It consumed him. There were many bike rides where he could go for three hours and talk about nothing but that."

"He definitely became a different person for a while," Hansen says. "Just so stressed out. Like it was sucking the joy out of his life."